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Estimated time of infection vs. confirmed infections

Following the ideas from Tomas Pueyo's Medium post "Coronavirus: Why You Must Act Now" [1], we assume the average time from infection to death at 23 days [2]. The data is pulled from the COVID-19 Data Repository by Johns Hopkins CSSE [3] every hour. Countries with a minimnum of 1000 confirmed cases and 40 confirmed deaths are included in this analysis.

The time from infection to death is equal to the incubation period plus the time from symptoms to death. This is used to estimate the time of the infections that lead to the observed deaths. We take the last fatality rate per country (total_cases/total_deaths) to estimate the number of infections that are responsible for the observed deaths.

In the figures below, you can observe successive waves of infections (dashed), detections (black) and deaths (red) for each country. The upper panel shows the absolute number of events. The dashed lines show the estimated number of infections. The lower panel shows the normalized number of events. Here the temporal delay between the waves and the relative change between each other can be observed.

[1] https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca

[2] https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus

[3] https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series

US
Brazil
India
Mexico
Peru
Russia
United Kingdom
Italy
Colombia
Indonesia
France
Argentina
Iran
Germany
Spain
South Africa
Poland
Ukraine
Turkey
Chile
Romania
Ecuador
Czechia
Philippines
Hungary
Canada
Belgium
Pakistan
Bangladesh
Tunisia
Iraq
Bulgaria
Netherlands
Bolivia
Portugal
Egypt
Paraguay
Japan
Sweden
Burma
Greece
Malaysia
Slovakia
Kazakhstan
Guatemala
Morocco
Switzerland
Austria
Nepal
Jordan
Bosnia and Herzegovina
Honduras
Saudi Arabia
Croatia
Lebanon
Thailand
Serbia
Afghanistan
Panama
Israel
Georgia
Moldova
Sri Lanka
Vietnam
Uruguay
North Macedonia
Costa Rica
Azerbaijan
Ireland
Algeria
Armenia
China
Ethiopia
Lithuania
Slovenia
Kenya
Zimbabwe
Cuba
Oman
Dominican Republic
Libya
Venezuela
West Bank and Gaza
Belarus
Zambia
Namibia
Uganda
Sudan
El Salvador
Latvia
Denmark
Albania
Kyrgyzstan
Kuwait
Kosovo
Nigeria
South Korea
Botswana
United Arab Emirates
Malawi
Syria
Mozambique
Cambodia
Montenegro
Senegal
Bahrain
Cameroon
Jamaica
Estonia
Trinidad and Tobago
Angola
Congo (Kinshasa)
Finland
Uzbekistan
Rwanda
Australia
Madagascar
Eswatini
Ghana
Somalia
Mongolia
Luxembourg
Taiwan*
Norway
Suriname
Mauritania
Qatar
Guyana
Haiti
Mali
Cyprus
Malta
Lesotho
Fiji
Cote d'Ivoire
Belize
Bahamas
Cabo Verde
Guinea
Maldives
Hong Kong
Nicaragua
Papua New Guinea
Congo (Brazzaville)
Burkina Faso
Gabon
Togo
Djibouti
Andorra
Tajikistan
South Sudan

Ahead of the curve

Some countries start testing the population earlier in the outbreak than others. The time delay between the wave of deaths and the wave of confirmed cases is indicative for how early a country is detecting new cases ahead of the increase of deaths. Earlier detection means a better chances for successful isolation of an infected person and treatment of the desease.

We measure the distance of the maximum of cumulative deaths and new deaths to the number of infections to estimate the progression of the infection across countries.

If, in the early phase of the infection wave, the number of deaths rises faster than the number of confirmed cases, the distance drops, indicating that

A comparison of countries with respect to their mean time for reponse is presented below.

To determine the above values, we plot the number of confirmed cases (solid black lines) and the number of deaths (dashed black lines). From this, we measure the distance of the day of maximum deaths (dashed red lines) to the day of confirmed cases at this y-value.

The distance is indicative for how fast the humber of confirmed cases increases comapred to the increase of the number of deaths.

US
Brazil
India
Mexico
Peru
Russia
United Kingdom
Italy
Colombia
Indonesia
France
Argentina
Iran
Germany
Spain
South Africa
Poland
Ukraine
Turkey
Chile
Romania
Ecuador
Czechia
Philippines
Hungary
Canada
Belgium
Pakistan
Bangladesh
Tunisia
Iraq
Bulgaria
Netherlands
Bolivia
Portugal
Egypt
Paraguay
Japan
Sweden
Burma
Greece
Malaysia
Slovakia
Kazakhstan
Guatemala
Morocco
Switzerland
Austria
Nepal
Jordan
Bosnia and Herzegovina
Honduras
Saudi Arabia
Croatia
Lebanon
Thailand
Serbia
Afghanistan
Panama
Israel
Georgia
Moldova
Sri Lanka
Vietnam
Uruguay
North Macedonia
Costa Rica
Azerbaijan
Ireland
Algeria
Armenia
China
Ethiopia
Lithuania
Slovenia
Kenya
Zimbabwe
Cuba
Oman
Dominican Republic
Libya
Venezuela
West Bank and Gaza
Belarus
Zambia
Namibia
Uganda
Sudan
El Salvador
Latvia
Denmark
Albania
Kyrgyzstan
Kuwait
Kosovo
Nigeria
South Korea
Botswana
United Arab Emirates
Malawi
Syria
Mozambique
Cambodia
Montenegro
Senegal
Bahrain
Cameroon
Jamaica
Estonia
Trinidad and Tobago
Angola
Congo (Kinshasa)
Finland
Uzbekistan
Rwanda
Australia
Madagascar
Eswatini
Ghana
Somalia
Mongolia
Luxembourg
Taiwan*
Norway
Suriname
Mauritania
Qatar
Guyana
Haiti
Mali
Cyprus
Malta
Lesotho
Fiji
Cote d'Ivoire
Belize
Bahamas
Cabo Verde
Guinea
Maldives
Hong Kong
Nicaragua
Papua New Guinea
Congo (Brazzaville)
Burkina Faso
Gabon
Togo
Djibouti
Andorra
Tajikistan
South Sudan